Nucleic Acids Biochemistry

  1. Structure and Diversity of Ribonucleic Acid (RNA)
    1. Primary Structure of RNA
      1. RNA Nucleotide Sequence
        1. Base Composition
          1. Sequence Variability
            1. Length Diversity
            2. 5' and 3' Ends
              1. Terminal Modifications
                1. Capping Structures
                  1. Polyadenylation
                2. Secondary Structure
                  1. Base Pairing in RNA
                    1. Watson-Crick Pairs
                      1. Wobble Base Pairs
                        1. Non-Standard Pairs
                        2. Stem-Loop Structures
                          1. Hairpin Formation
                            1. Loop Sequences
                              1. Stability Factors
                              2. Bulges and Mismatches
                                1. Single-Base Bulges
                                  1. Multi-Base Bulges
                                    1. Internal Loops
                                    2. Pseudoknots
                                      1. Formation Mechanism
                                        1. Structural Complexity
                                          1. Functional Significance
                                          2. Kissing Loops
                                            1. Loop-Loop Interactions
                                              1. Tertiary Structure Formation
                                            2. Tertiary Structure
                                              1. RNA Folding Principles
                                                1. Hierarchical Folding
                                                  1. Cooperative Interactions
                                                    1. Kinetic vs Thermodynamic Control
                                                    2. Stabilizing Interactions
                                                      1. Base Stacking Forces
                                                        1. Metal Ion Coordination
                                                          1. Hydrogen Bonding Networks
                                                            1. Electrostatic Interactions
                                                            2. Examples of Complex Tertiary Structures
                                                              1. tRNA L-Shape
                                                                1. Ribosomal RNA Architecture
                                                                  1. Ribozyme Active Sites
                                                                2. Major Classes of RNA and Their Functions
                                                                  1. Messenger RNA
                                                                    1. Structure and Features
                                                                      1. 5' Untranslated Region
                                                                        1. Coding Sequence
                                                                          1. 3' Untranslated Region
                                                                            1. Poly(A) Tail
                                                                            2. Function in Protein Coding
                                                                              1. Genetic Information Transfer
                                                                                1. Translation Template
                                                                                  1. Regulatory Elements
                                                                                  2. mRNA Processing
                                                                                    1. Capping
                                                                                      1. Splicing
                                                                                        1. Polyadenylation
                                                                                      2. Transfer RNA
                                                                                        1. Cloverleaf Structure
                                                                                          1. Secondary Structure Pattern
                                                                                            1. Conserved Regions
                                                                                              1. Variable Regions
                                                                                              2. L-Shaped Tertiary Structure
                                                                                                1. Three-Dimensional Folding
                                                                                                  1. Functional Domains
                                                                                                  2. Acceptor Stem
                                                                                                    1. 3' CCA Sequence
                                                                                                      1. Amino Acid Attachment Site
                                                                                                      2. D Loop
                                                                                                        1. Dihydrouridine Modifications
                                                                                                          1. Structural Role
                                                                                                          2. Anticodon Loop
                                                                                                            1. Codon Recognition
                                                                                                              1. Wobble Position
                                                                                                                1. Modified Bases
                                                                                                                2. TψC Loop
                                                                                                                  1. Pseudouridine Content
                                                                                                                    1. Ribosome Binding
                                                                                                                    2. Aminoacylation Process
                                                                                                                      1. Synthetase Recognition
                                                                                                                        1. ATP Requirement
                                                                                                                          1. Proofreading Mechanisms
                                                                                                                        2. Ribosomal RNA
                                                                                                                          1. Structure and Domains
                                                                                                                            1. Small Subunit rRNA
                                                                                                                              1. Large Subunit rRNA
                                                                                                                                1. Conserved Regions
                                                                                                                                  1. Variable Regions
                                                                                                                                  2. Role in Ribosome Function
                                                                                                                                    1. Peptidyl Transferase Activity
                                                                                                                                      1. Decoding Center Function
                                                                                                                                        1. Structural Framework
                                                                                                                                      2. Small Nuclear RNA
                                                                                                                                        1. U1 snRNA Function
                                                                                                                                          1. U2 snRNA Function
                                                                                                                                            1. U4/U6 snRNA Complex
                                                                                                                                              1. U5 snRNA Function
                                                                                                                                                1. Role in Splicing
                                                                                                                                                  1. Spliceosome Assembly
                                                                                                                                                    1. Splice Site Recognition
                                                                                                                                                      1. Catalytic Function
                                                                                                                                                    2. MicroRNA
                                                                                                                                                      1. Biogenesis Pathway
                                                                                                                                                        1. Primary Transcript Processing
                                                                                                                                                          1. Precursor miRNA Formation
                                                                                                                                                            1. Mature miRNA Generation
                                                                                                                                                            2. Role in Gene Regulation
                                                                                                                                                              1. Target mRNA Recognition
                                                                                                                                                                1. Translation Repression
                                                                                                                                                                  1. mRNA Degradation
                                                                                                                                                                2. Small Interfering RNA
                                                                                                                                                                  1. Biogenesis Pathway
                                                                                                                                                                    1. Double-Strand RNA Processing
                                                                                                                                                                      1. Dicer Activity
                                                                                                                                                                        1. RISC Loading
                                                                                                                                                                        2. Role in RNA Interference
                                                                                                                                                                          1. Target Recognition
                                                                                                                                                                            1. mRNA Cleavage
                                                                                                                                                                              1. Chromatin Modification
                                                                                                                                                                            2. Long Non-coding RNA
                                                                                                                                                                              1. Types and Classifications
                                                                                                                                                                                1. Intergenic lncRNA
                                                                                                                                                                                  1. Antisense lncRNA
                                                                                                                                                                                    1. Intronic lncRNA
                                                                                                                                                                                    2. Functions
                                                                                                                                                                                      1. Transcriptional Regulation
                                                                                                                                                                                        1. Chromatin Modification
                                                                                                                                                                                          1. Post-Transcriptional Control
                                                                                                                                                                                            1. Protein Scaffolding
                                                                                                                                                                                          2. Other RNA Classes
                                                                                                                                                                                            1. Small Nucleolar RNA
                                                                                                                                                                                              1. PIWI-Interacting RNA
                                                                                                                                                                                                1. Enhancer RNA
                                                                                                                                                                                                  1. Circular RNA
                                                                                                                                                                                                2. Catalytic RNA: Ribozymes
                                                                                                                                                                                                  1. Types of Ribozymes
                                                                                                                                                                                                    1. Group I Introns
                                                                                                                                                                                                      1. Group II Introns
                                                                                                                                                                                                        1. RNase P
                                                                                                                                                                                                          1. Hammerhead Ribozymes
                                                                                                                                                                                                            1. Hairpin Ribozymes
                                                                                                                                                                                                              1. Peptidyl Transferase Center
                                                                                                                                                                                                              2. Mechanisms of Catalysis
                                                                                                                                                                                                                1. Metal Ion Catalysis
                                                                                                                                                                                                                  1. Acid-Base Catalysis
                                                                                                                                                                                                                    1. Electrostatic Stabilization
                                                                                                                                                                                                                      1. Conformational Changes
                                                                                                                                                                                                                      2. Biological Roles
                                                                                                                                                                                                                        1. RNA Processing
                                                                                                                                                                                                                          1. Protein Synthesis
                                                                                                                                                                                                                            1. Gene Regulation
                                                                                                                                                                                                                              1. Evolutionary Significance

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                                                                                                                                                                                                                          3. Structure of Deoxyribonucleic Acid (DNA)

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                                                                                                                                                                                                                          5. Nucleic Acid Metabolism: Biosynthesis